Originated as a term used by hackers to describe gaining possession of a system, having hacked a box and got root they basically control it as much as if it was theirs, thus it could be considered owned by them. From this it was encorporated into the cultures vernacular including the limited(and awkward to type) vocabulary of so called l33t speak(0wn3d) Would-be hackers would come to use the phrase when taking someone out with a ping flood or other DoS attack, and although no access to the victim's system (typically another newbie hanging around on the same irc channel speaking in numbers) was gained yet they were still said to be owned. From there is came to simply mean bettering (or fucking over) someone and was even used to describe non-computer based events as described in the many other definitions. Though now its most common in CS games when someone kills you...

With the original use of the word it would seem most people I see using XP dont even own their own system :p

To be defeated in a computer game, causing the winner's ego to inflate like a party balloon as if such a victory has any tangible significance outside that of his stinking socks-infested dorm room. These people will frequently create animated GIFs of violent sports events where a player gets clobbered by his opponent, complete with blinking neon "PWN3D!" captions, and post them on their blogs to indicate that they should not be messed with.

Person A: Dude, totally like you sooo suck so much, I PWNZ0RED J00!!!!11!!11